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- PDB-7b04: Structure of Nitrite oxidoreductase (Nxr) from the anammox bacter... -

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Basic information

Entry
Database: PDB / ID: 7b04
TitleStructure of Nitrite oxidoreductase (Nxr) from the anammox bacterium Kuenenia stuttgartiensis.
Components(Nitrite oxidoreductase subunit ...) x 3
KeywordsOXIDOREDUCTASE / Metalloprotein / Anammox
Function / homology
Function and homology information


nitrate reductase / anammoxosome / nitrate reductase activity / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding / periplasmic space / heme binding / metal ion binding
Similarity search - Function
DMSO reductase family, type II, haem b-binding subunit / Cytochrome c-552/DMSO reductase-like, haem-binding domain / Ethylbenzene dehydrogenase / 4Fe-4S dicluster domain / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Twin arginine translocation (Tat) signal profile. ...DMSO reductase family, type II, haem b-binding subunit / Cytochrome c-552/DMSO reductase-like, haem-binding domain / Ethylbenzene dehydrogenase / 4Fe-4S dicluster domain / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
FE3-S4 CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / Chem-MD1 / MOLYBDENUM ATOM / IRON/SULFUR CLUSTER / Nitrite oxidoreductase subunit C / Nitrite oxidoreductase subunit B / Nitrite oxidoreductase subunit A
Similarity search - Component
Biological speciesKuenenia stuttgartiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.97 Å
AuthorsMoreno-Chicano, T. / Dietl, A. / Akram, M. / Barends, T.R.M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)724362European Union
CitationJournal: Nat Microbiol / Year: 2021
Title: Structural and functional characterization of the intracellular filament-forming nitrite oxidoreductase multiprotein complex
Authors: Chicano, T.M. / Dietrich, L. / de Almeida, N.M. / Akram, M. / Hartmann, E. / Leidreiter, F. / Leopoldus, D. / Mueller, M. / Sanchez, R. / Nuijten, G.H.L. / Reimann, J. / Seifert, K.A. / ...Authors: Chicano, T.M. / Dietrich, L. / de Almeida, N.M. / Akram, M. / Hartmann, E. / Leidreiter, F. / Leopoldus, D. / Mueller, M. / Sanchez, R. / Nuijten, G.H.L. / Reimann, J. / Seifert, K.A. / Schlichting, I. / van Niftrik, L. / Jetten, M.S.M. / Dietl, A. / Kartal, B. / Parey, K. / Barends, T.R.M.
History
DepositionNov 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitrite oxidoreductase subunit B
B: Nitrite oxidoreductase subunit A
C: Nitrite oxidoreductase subunit C
D: Nitrite oxidoreductase subunit B
E: Nitrite oxidoreductase subunit A
F: Nitrite oxidoreductase subunit C
G: Nitrite oxidoreductase subunit B
H: Nitrite oxidoreductase subunit A
I: Nitrite oxidoreductase subunit C
J: Nitrite oxidoreductase subunit B
K: Nitrite oxidoreductase subunit A
L: Nitrite oxidoreductase subunit C
M: Nitrite oxidoreductase subunit B
N: Nitrite oxidoreductase subunit A
O: Nitrite oxidoreductase subunit C
P: Nitrite oxidoreductase subunit B
Q: Nitrite oxidoreductase subunit A
R: Nitrite oxidoreductase subunit C
S: Nitrite oxidoreductase subunit B
T: Nitrite oxidoreductase subunit A
U: Nitrite oxidoreductase subunit C
V: Nitrite oxidoreductase subunit B
W: Nitrite oxidoreductase subunit A
X: Nitrite oxidoreductase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,756,016112
Polymers1,724,20724
Non-polymers31,80888
Water14,394799
1
A: Nitrite oxidoreductase subunit B
B: Nitrite oxidoreductase subunit A
C: Nitrite oxidoreductase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,50214
Polymers215,5263
Non-polymers3,97611
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25130 Å2
ΔGint-231 kcal/mol
Surface area50360 Å2
MethodPISA
2
D: Nitrite oxidoreductase subunit B
E: Nitrite oxidoreductase subunit A
F: Nitrite oxidoreductase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,50214
Polymers215,5263
Non-polymers3,97611
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21920 Å2
ΔGint-248 kcal/mol
Surface area65590 Å2
MethodPISA
3
G: Nitrite oxidoreductase subunit B
H: Nitrite oxidoreductase subunit A
I: Nitrite oxidoreductase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,50214
Polymers215,5263
Non-polymers3,97611
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25210 Å2
ΔGint-229 kcal/mol
Surface area50420 Å2
MethodPISA
4
J: Nitrite oxidoreductase subunit B
K: Nitrite oxidoreductase subunit A
L: Nitrite oxidoreductase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,50214
Polymers215,5263
Non-polymers3,97611
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25390 Å2
ΔGint-230 kcal/mol
Surface area50790 Å2
MethodPISA
5
M: Nitrite oxidoreductase subunit B
N: Nitrite oxidoreductase subunit A
O: Nitrite oxidoreductase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,50214
Polymers215,5263
Non-polymers3,97611
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25070 Å2
ΔGint-251 kcal/mol
Surface area50030 Å2
MethodPISA
6
P: Nitrite oxidoreductase subunit B
Q: Nitrite oxidoreductase subunit A
R: Nitrite oxidoreductase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,50214
Polymers215,5263
Non-polymers3,97611
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25210 Å2
ΔGint-232 kcal/mol
Surface area50420 Å2
MethodPISA
7
S: Nitrite oxidoreductase subunit B
T: Nitrite oxidoreductase subunit A
U: Nitrite oxidoreductase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,50214
Polymers215,5263
Non-polymers3,97611
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25320 Å2
ΔGint-221 kcal/mol
Surface area50650 Å2
MethodPISA
8
V: Nitrite oxidoreductase subunit B
W: Nitrite oxidoreductase subunit A
X: Nitrite oxidoreductase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,50214
Polymers215,5263
Non-polymers3,97611
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24970 Å2
ΔGint-233 kcal/mol
Surface area50280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.626, 206.467, 527.141
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Nitrite oxidoreductase subunit ... , 3 types, 24 molecules ADGJMPSVBEHKNQTWCFILORUX

#1: Protein
Nitrite oxidoreductase subunit B / / Strongly similar to nitrate reductase (NarH)


Mass: 48013.816 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Kuenenia stuttgartiensis (bacteria) / References: UniProt: Q1PZD5, nitrate reductase
#2: Protein
Nitrite oxidoreductase subunit A / / Similar to nitrate reductase subunit NarG


Mass: 131907.141 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Kuenenia stuttgartiensis (bacteria) / References: UniProt: Q1PZD8, nitrate reductase
#3: Protein
Nitrite oxidoreductase subunit C /


Mass: 35604.953 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Kuenenia stuttgartiensis (bacteria) / References: UniProt: Q1PZD4

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Non-polymers , 7 types, 887 molecules

#4: Chemical...
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe3S4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-MD1 / PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER


Mass: 740.557 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-MO / MOLYBDENUM ATOM


Mass: 95.940 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mo / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 799 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 13% PEG 4000 50 mM TrisCl pH 8.5 1.8 mM n-Decyl-beta-D-maltoside

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.7345 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7345 Å / Relative weight: 1
ReflectionResolution: 2.97→206.47 Å / Num. obs: 377277 / % possible obs: 96.7 % / Redundancy: 26.3 % / Biso Wilson estimate: 49.7 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.428 / Rpim(I) all: 0.12 / Rrim(I) all: 0.444 / Net I/σ(I): 9.6
Reflection shellResolution: 2.97→3.07 Å / Redundancy: 20.6 % / Rmerge(I) obs: 2.48 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 18807 / CC1/2: 0.498 / Rpim(I) all: 0.786 / Rrim(I) all: 2.608 / % possible all: 62.1

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Processing

Software
NameVersionClassification
PHENIXv1.14rc1refinement
XDSdata reduction
STARANISOv3.000data scaling
PHENIXv1.14rc1phasing
RefinementMethod to determine structure: SAD / Resolution: 2.97→192.25 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.255 21282 5.64 %in shells
Rwork0.223 ---
obs0.225 377164 95.4 %-
Displacement parametersBiso mean: 47 Å2
Refinement stepCycle: LAST / Resolution: 2.97→192.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms113616 0 1432 799 115847

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